Genome-wide DNA Methylation Profiling Reveals Methylation Markers Associated with 3q Gain for Detection of Cervical Precancer and Cancer

Clin Cancer Res. 2017 Jul 15;23(14):3813-3822. doi: 10.1158/1078-0432.CCR-16-2641. Epub 2017 Jan 24.


Purpose: Epigenetic host cell changes involved in cervical cancer development following a persistent high-risk human papillomavirus (hrHPV) infection, provide promising markers for the management of hrHPV-positive women. In particular, markers based on DNA methylation of tumor suppressor gene promoters are valuable. These markers ideally identify hrHPV-positive women with precancer (CIN2/3) in need of treatment. Here, we set out to identify biologically relevant methylation markers by genome-wide methylation analysis of both hrHPV-transformed cell lines and cervical tissue specimens.Experimental Design and Results: Genome-wide discovery by next-generation sequencing (NGS) of methyl-binding domain-enriched DNA (MBD-Seq) yielded 20 candidate methylation target genes. Further verification and validation by multiplex-targeted bisulfite NGS and (quantitative) methylation-specific PCR (MSP) resulted in 3 genes (GHSR, SST, and ZIC1) that showed a significant increase in methylation with severity of disease in both tissue specimens and cervical scrapes (P < 0.005). The area under the ROC curve for CIN3 or worse varied between 0.86 and 0.89. Within the group of CIN2/3, methylation levels of all 3 genes increased with duration of lesion existence (P < 0.0005), characterized by duration of preceding hrHPV infection, and were significantly higher in the presence of a 3q gain (P < 0.05) in the corresponding tissue biopsy.Conclusions: By unbiased genome-wide DNA methylation profiling and comprehensive stepwise verification and validation studies using in vitro and patient-derived samples, we identified 3 promising methylation markers (GHSR, SST, and ZIC1) associated with a 3q gain for the detection of cervical (pre)cancer. Clin Cancer Res; 23(14); 3813-22. ©2017 AACR.

MeSH terms

  • Biomarkers, Tumor / genetics
  • Cell Line, Tumor
  • Chromosomes, Human, Pair 3 / genetics
  • DNA Methylation / genetics*
  • Female
  • Genome, Human
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Papillomaviridae / pathogenicity
  • Precancerous Conditions / genetics*
  • Precancerous Conditions / pathology
  • Receptors, Ghrelin / genetics*
  • Somatostatin / genetics*
  • Transcription Factors / genetics*
  • Uterine Cervical Neoplasms / genetics*
  • Uterine Cervical Neoplasms / pathology


  • Biomarkers, Tumor
  • Receptors, Ghrelin
  • Transcription Factors
  • ZIC1 protein, human
  • Somatostatin